I don't speak Cebuano, but in Tagalog, when you are addressing someone directly, you don't use "si".
Kumusta si Sam? = How is Sam?
Kumusta kay Sam. = Say hello to Sam for me.
Kumusta, Sam? = Though this may also be understood as "How are you, Sam?", it may be said to simply mean, "Hi/Hello, Sam!
Kumusta ka, Sam? = How are you, Sam?